Recent developments in the MAFFT multiple sequence alignment program

By Kazutaka Katoh, Hiroyuki Toh. 2008

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In Molecular Biology

Citations in the corpus

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability (2013, methodology): “After reviewing the previous version (version 6) in Katoh and Toh (2008b), we have been continuously improving its accuracy, speed, and utility in practical situations.”
Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein (2013, methodology): “gram (Katoh and Toh 2008), and a conservation score for each site”
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs (2012, methodology): “using MAFFT (43), and filtered using TrimAl (44), and corroborated with known taxonomies from the literature.”
Phylogeny and classification of Cucujoidea and the recognition of a new superfamily Coccinelloidea (Coleoptera: Cucujiformia) (2015, methodology): “Alignment of ribosomal genes was achieved using the mafft 6.5 webserver (Katoh & Toh, 2008) (http://align.bmr.kyushu-u.ac.jp/mafft/online/server) using the G-INS-i search strategy.”
metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data (2015, methodology): “Cases that cannot unambiguously be assigned to archaea, bacteria, eu-karyota, mitochondria or chloroplast origin are aligned to their ﬁve best BLAST matches using MAFFT (Katoh & Toh 2008) to facilitate further manual examination.”
Moyamoya disease factor RNF213 is a giant E3 ligase with a dynein-like core and a distinct ubiquitin-transfer mechanism (2020, background): “weight adjustment, and BLOSUM62 as the scoring matrix (Katoh and Toh, 2008; Pei and Grishin, 2001).”
A Molecular Phylogeny of Living Primates (2011, methodology): “DNA Sequence Analyses Multiple sequence files for each gene segment amplified were aligned by MAFFT version 6 [69,70], imported into Se-Al ver Figure 2.”
Towards a revised generic classification of lecanoroid lichens (Lecanoraceae, Ascomycota) based on molecular, morphological and chemical evidence (2016, methodology): “Sequences of each locus were aligned using the program MAFFT v7 (Katoh et al. 2009; Katoh and Toh 2008).”
Phylogeny and evolution of Staphyliniformia and Scarabaeiformia: forest litter as a stepping stone for diversification of nonphytophagous beetles (2015, methodology): “8 (Katoh et al., 2002; Katoh & Toh, 2008) with default alignment parameters and then refined manually in Mesquite v2.”
Revisiting the insect mitochondrial molecular clock: the mid-Aegean trench calibration. (2010, positive): “240 (Katoh et al. 2005; Katoh and Toh 2008).”
Disturbance and diversity of wood-inhabiting fungi: effects of canopy gaps and downed woody debris (2014, methodology): “6 (Katoh and Toh 2008) and phylogenetic reconstruction of ITS sequences was performed in MEGA v.”
Long‐term experimental manipulation of climate alters the ectomycorrhizal community of Betula nana in Arctic tundra (2011, methodology): “Phylogenetic analyses were based on MAFFT version 6 (Katoh, 2008) alignments of fungal sequences.”